|Datasets (QC pass)
In this ReMap 2020 human release we have manually curated and annotated 6,498 ChIP-seq experiments, retained after quality control 5,798 datasets and, for the first time, we included one large ChIP-exo experiment GSE78099 from Imbeault M. et al Nature 2017. We applied our pipeline for both type of data, however most postprocessing steps applied by Imbeault M. et al Nature 2017 where applied to the ChIP-exo data.After consistent peak calling, we identified a total of 164.7 million peaks bound by transcriptionnal regulators (including 990,476 peaks from ChIP-exo). These numbers include overlapping sites for identical TRs which were studied in various conditions. To address this we merged overlapping TR peaks for similar TR obtaining a catalog of 75 million non-redundant peaks.
A link to the UCSC Genome Browser was also added to facilitate genomic integration of the binding sites with other genome annotations. Our BED tracks allow for the visualization of our catalogues of binding sites on the human genome. Finally, different analyses such as the quality of datasets and DNA constraint analysis are provided for each transcription factor.
The ReMap BED files are available to download either for a given transcriptional regulator, by Biotype or for the entire catalog as one very large BED file.
For Homo sapiens the GRCh38/hg38 assembly is currently the supported assembly, but our files can be lifted to hg19 with liftover. We also provide an archive of the ReMap 2018 and 2015 catalogs.
For Arabidopsis thaliana we provide BED files for transcriptional regulators, histones marks, ecotypes and biotype coupled with a given ecotype. The TAIR10 assembly is the only assembly supported by ReMap.